This SuperSeries is composed of the SubSeries listed below.
Embryonic stem cell potency fluctuates with endogenous retrovirus activity.
Specimen part, Cell line, Treatment
View SamplesWe compared gene expression from 2C::tomato+/- ES cells from Kdm1a wt and mutant ES cultures
Embryonic stem cell potency fluctuates with endogenous retrovirus activity.
Cell line
View SamplesTo determine gene expression in 2 cell stage embryos Overall design: 3 Replicates of litters of wild type 2 cell stage embryos
Embryonic stem cell potency fluctuates with endogenous retrovirus activity.
Specimen part, Subject
View SamplesTo measure gene expression difference between wt and g9A knockout ES cells Overall design: G9A TT2 ES cells (Yokochi et al) were treated with Veh. Or 4OHT (to delete G9A)
Embryonic stem cell potency fluctuates with endogenous retrovirus activity.
Specimen part, Treatment, Subject
View SamplesWe identified/quantified genes and repeat elements enriched within 2C::tomato+ cells vs. 2C::tomato - cells Overall design: 2C::tomato + and - cells were collected by FACS for RNA-Seq analysis
Embryonic stem cell potency fluctuates with endogenous retrovirus activity.
Specimen part, Subject
View SamplesTo investigate the function of CITED1 in melanoma, its expression was transiently down regulated using CITED1-targeting siRNA. The HT144 melanoma cell line was chosen as it had a relatively high level of detectable CITED1 mRNA and protein expression.
Loss of CITED1, an MITF regulator, drives a phenotype switch in vitro and can predict clinical outcome in primary melanoma tumours.
Cell line
View Samples4 replicates were prepared from A2058 melanoma cells [transfected with 10ng of empty vector (pcDNA3.1+)] and treated with 5ng/ml TGF1 or vehicle control for 24hrs
Loss of CITED1, an MITF regulator, drives a phenotype switch in vitro and can predict clinical outcome in primary melanoma tumours.
Cell line, Treatment
View SamplesBecause it excises thymine from GT mismatches, TDG was proposed to counter mutagenesis by 5-methylcytosine deamination. Yet, TDG was also observed to attack 5-methycytosine itself, making it a candidate DNA demethylase, and interactions with transcription factors implicated additional functions in gene regulation. Unlike other DNA glycosylases, TDG is essential for embryonic development. Fibroblasts from Tdg null embryos show massively impaired gene regulation, and this correlates with imbalanced histone modification and CpG methylation. TDG associates with the promoters of affected genes in MEFs and in embryonic stem cells, but epigenetic aberrations appear only in differentiated cells. TDG also contributes to the maintenance of active and bivalent chromatin during cell differentiation, using its DNA glycosylase activity to counter aberrant de novo methylation. Thus, TDG dependent DNA repair stabilizes epigenetic states during cell differentiation.
Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.
Specimen part
View SamplesGEP class prediction in association with CI-FISH (42 candidate genes) and patient MRD stratification
Linking genomic lesions with minimal residual disease improves prognostic stratification in children with T-cell acute lymphoblastic leukaemia.
Specimen part, Disease, Disease stage
View SamplesAnalysis of transcriptional changes upon persistent heat stress with emphasis on epigenetically regulated genes
Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis.
Specimen part
View Samples